


Broke through all of my confusion.

by everydaytomholland



Series: Pangs [4]
Category: Iron Man (Movies), Marvel Cinematic Universe, Spider-Man - All Media Types
Genre: Brain Damage, Fluff and Angst, Irondad & Spiderson, Medical Inaccuracies, Other, Peter Parker Needs a Hug, Spiderbite, Tony Stark Needs a Hug, Traumatic Brain Injury
Language: English
Status: Completed
Published: 2018-09-23
Updated: 2018-09-23
Packaged: 2019-07-15 20:51:22
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 1
Words: 4,035
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/16071101
Author URL: https://archiveofourown.org/users/everydaytomholland/pseuds/everydaytomholland
Summary: Re-imagining of Iron Man 1 and beyond where Peter is Tony's son. Obie is not a nice man.





	Broke through all of my confusion.

**Author's Note:**

> ***DISCLAIMER: This is in no way intended to be ableist, the idea popped into my head that if the spiderbite could repair Peter's crappy eyesight, then could it repair a traumatic brain injury as well? Then boom, this fic was born***
> 
> Title comes from the Kelly Clarkson song, "You found me."

Tony Stark never really hid the fact that he had a 7 year old son, he just hadn’t publicised it either. But when he came home from three months in captivity in Afghanistan, there was no way he wasn’t seeing Peter the moment he touched down. The press had seen their tearful reunion and the rest was history. 

It had been easy over the years for Tony to keep Peter hidden with minimal effort; he lived half the time with his Aunt May and Uncle Ben (his mom’s sister and her husband) and took their last name, ‘Parker’, for his safety. It also allowed Tony to spend half of his time in New York and half in California running the company and giving the appearance that he was carrying on with his playboy lifestyle. The truth was that he hadn’t touched alcohol since Peter was born, but was happy to keep up pretences in order to protect his son. 

It had been unavoidable when he was back after being held hostage though. Just hours after getting home he made a press conference; both to announce the end of weapons production by Stark Industries, but also to ask that the press respect the privacy of his son. Maybe it was because he’d been held captive and tortured by terrorists for three months, but the press were actually very respectful of his wishes; though he suspected Pepper may have had something to do with that. 

This relief from the press allowed him to work on his suit in his spare time – either when Peter was at his other home or after he went to bed at night. Despite what Rhodey and the Department of Defense thought, his suit wasn’t intended to be a weapon, it was more of a suit of armour. 

Tony was more aware of the goings on in his company than people realised or gave him credit for. He knew that someone was trying to continue weapons production behind his back, and he thought he knew who, he just had to prove it. He was glad when Pepper came over that afternoon, before Peter got home from school. It took a bit of convincing but he got her to agree to go into SI offices and get him the encrypted files; now it was a waiting game. 

Peter was a sensitive kid and always young for his age, the days when he had gym at school he always came home exhausted and would go straight to bed after dinner. It was just after he’d tucked his son in that Pepper’s call came through. He pressed answer but before he had the chance to say anything he heard a whirring and his body went rigid and the phone fell out of his hand. He could barely hear Obadiah talking over the pounding of his heartbeat in his head, but he felt the pain of the arc reactor being ripped from his chest. Obie hadn’t even left the room yet before Tony lost consciousness. 

Peter was a sensitive kid. He’d always been keenly attuned to what other people were feeling and seemed to instinctively know when something was wrong. It was this that had the little boy waking up, looking for his father when he bumped into uncle Obie. He didn’t know why, but something about the man’s smile scared him in a way it never had before. Obie ushered them back into Peter’s bedroom. Peter was barely able to get a word out before Obie pushed him to the ground and started kicking him. He attempted to protect himself from the painful kicks but it was useless, several kicks to the head and he was unconscious. But Obie kept kicking him. He only realised that he may have gone too far when he saw the blood coming from the young boy’s ear. He didn’t linger though, he had more important things to worry about. 

When Rhodey arrived at Stark tower, he found Tony unconscious in the living room. He managed to rouse him enough to understand that he needed to get the arc reactor from the lab. Tony still looked sick but rushed off to stop Obadiah, Rhodey following close behind. 

It wasn’t until Obie was dead and Tony was being patched up by paramedics that he remembered with a panic that his son had been at the tower. Suddenly not caring in the slightest that he had a mild concussion. He arrived at the tower in record time only to have his worst dreams realised. 

Peter was in his room, on the floor next to his bed. His tiny body seemed to be absolutely covered in bruises and there was blood surrounding his head. Supressing his panic, Tony gingerly picked up his son and rushed him to the nearest emergency room. 

It was a long night, most of which had seen Peter in the operating room trying to relieve the pressure in his brain and had left him in a coma. Pepper had tried to tell Tony that he didn’t need to be at the press conference, but he had insisted. That Agent Coulson guy had given Tony the alibi he was supposed to read out, but he wasn’t interested. 

“I was supposed to get up here today and tell you that there was just an accident at Stark Industries last night, that I was on a yacht partying with friends, but that’s not true. Obadiah Stane, one of my most trusted advisors, betrayed me. He tried to kill me, so I went after him. The truth is: I am Iron Man.” There was an uproar. “Please, I’m almost done. I wasn’t going to reveal my identity, I honestly wasn’t. But last night, Obie almost killed my son. Right now he’s in a coma, fighting for his life, and I needed people to know that I’m not letting anyone come after my family ever again.”

He didn’t linger after the press conference ended. He went back to the hospital, sitting on one side of the bed that was far too big for his tiny son, May and Ben were sitting on the other side. The only sounds in the room were the beeping of the heart monitor and the hissing of the ventilator. They had to wait for the swelling in Peter’s brain to go down to know what kind of damage there was. 

Tony had hoped that would be the worst of it, but he was wrong. Several days later, once the swelling had gone down, they did a series of tests on the still-comatose young boy. Brain damage. The words rang in Tony’s head hours after the doctor had uttered them. They wouldn’t know the extent of the damage until they were able to bring Peter out of the coma. For someone as impatient at Tony, this waiting was the worst part. 

Two weeks later, Peter woke up. It was rough. He was scared, confused, and barely seemed to be able to control his body, let alone talk. Tony couldn’t help but be glad that the boy did at least seem to recognise his family, almost immediately snuggling into his father’s side. There was going to be a long road ahead for him. 

Tony was glad that when he started getting sick from the palladium, Peter was still in hospital undergoing intense rehabilitation. In just a few months he’d improved considerably. He was sitting up by himself, and could usually feed himself for about half of all of his meals before he wore himself out. Their next goal was walking which Tony knew the boy was excited for. The hardest part though was his speech. Despite almost daily exercises with a speech pathologist, Peter could only utter a handful of words which, considering the boy seemed to be otherwise perfectly cognizant, was endlessly frustrating. 

It was hard for Tony to watch, which was why he didn’t put up much of a fight when May and Ben insisted that he continue with the plans for the Stark Expo. He’d be lying if he said that there wasn’t a small part of him that welcomed the distraction of Hammer and Vanko – especially once he knew he wasn’t going to die from palladium poisoning. If he was honest, he actually liked being the hero that the media portrayed Iron Man as. What was even better was that at the end of that ordeal, he got Pepper. 

Pepper fit into their lives so easily, and seemed to really care for and enjoy being another support for Peter. And slowly, the boy made progress. When he was finally discharged from hospital 18 months after Tony had gotten back from Afghanistan, he walked out of the hospital. Granted, he seemed to have a permanent limp and still stumbled over more than half of his words; but he was well enough that he could continue his therapy from the comfort of home. 

The next year was hard for Peter. He went back to school and was grateful that he was smart because he struggled with his handwriting. As the year wore on, Peter sunk into a bit of a depression. He never said anything to his dad about it, but he had expected to continue to make progress with his physical therapy. Instead, after a few months he had plateaued. He was frustrated, he just wanted things to be like they were before his dad was kidnapped. 

Peter was at Stark Tower when the Avengers were formed. Agent Coulson had come to speak to his dad and he spent the next few days with just him, Pepper and Happy while his dad was dealing with superhero stuff. His dad would’ve sent him to Queens to be with his aunt and uncle but they were taking their first holiday alone since Peter had been born and were currently on a beach in the Caribbean.

When Loki arrived at the tower, Peter was in his room playing with Lego. No one else was in the residential part of the tower: Pepper was at work and Happy had ducked out to run some errands. Peter was almost completely oblivious to everything going on outside of his bedroom. Until he happened to look up and see an alien flying past his window. 

By the time he mustered up the courage to venture outside his room, he found Loki lying stunned in the crater that the Hulk had left him in.  
“Who’re you?” Peter asked before he could stop himself. He usually didn’t like talking in front of strangers, very aware of the fact that his words were still very slurred after three years of speech therapy.  
“I am Loki of Asgard. Who are you?” The last thing the god of mischief had expected to see up here was a child.  
“I’m Peter. Are you hurt?” Loki was stunned at this. The boy seemed genuinely concerned about his welfare. He didn’t recall the last time he’d been shown this much compassion, least of all from a complete stranger.  
“No, I am not hurt.” Peter seemed satisfied with this answer and shuffled over to sit next to Loki; but the god didn’t miss his unusual gait. “Are you hurt, Peter?”  
“I-I was hurt. A few years ago. I’m not going to get better.” Loki didn’t miss the way Peter seemed to curl in on himself at these words.  
“You are ashamed,” it wasn’t a question, “why?”  
“Coz I’m a freak.” Peter muttered.  
“You are a warrior. I do not know how it is on Earth, but on Asgard you would be hailed a hero, and wear your battle scars with pride.” Loki didn’t know what it was about this small boy that gave him so much power over him, but he was happy when he saw that his words caused the boy to smile. 

Peter had no idea that while he was chatting to Loki, his father had almost died. 

That was how the Avengers found them. To say they were shocked was an understatement, but they walked in from the balcony and found their nemesis sitting on the sofa telling Iron Man’s 10 year old son stories about Asgard and his adventures with Thor as children. The boy was enraptured with this fantastical planet and didn’t notice his father and the other Avengers walking in, but Loki did. He turned to them and raised his hands in a gesture of surrender; “I’ll take that drink now.”

Even with the resulting PTSD from his brush with death, Tony found it hard to be mad at Loki when he saw the profound effect he’d had on Peter. He didn’t know the details of their conversation, but Peter’s demeanour had improved drastically and he was closer than he’d even been to the boy he was before the traumatic brain injury. 

Once Peter upgraded to middle school, he was allowed to take in a computer for taking notes instead of having to handwrite them all, and this allowed him to truly flourish. Much like his father, Peter was a genius, and now that his limited motor skills weren’t slowing him down, he was miles ahead of his classmates. 

Peter’s physical limitations hadn’t improved since he was 10, but he honestly didn’t mind, his dad and the school allowed him to skip gym which was a relief because he didn’t want to embarrass himself. 

Peter didn’t really have many friends. He only really had Ned. Ned had moved to New York from Hawaii and started at Peter’s school the same week that Peter finally started again. The two boys were instant best friends. Tony liked Ned, he was a sweet boy with good parents. He was good for Peter too, so if he donated anonymous scholarships so that the boy could attend the same middle school and high school as his son, was it really that big of a deal?

Tony was glad that the week everything went down with Ultron, Peter was staying in Queens. That didn’t stop in from checking in with his son before heading for Sokovia. The almost 15 year old had spent the day on a school trip to Oscorp, much to Tony’s annoyance, to check out their labs. When he saw Peter that evening, the boy claimed he wasn’t feeling well and thought he was coming down with the flu. Little did Tony know, by the time he returned from Sokovia, things would be completely different. 

It had been a terrible few days. Tony was so wracked with guilt over everything that had happened in Sokovia, he knew the fallout would be massive, but right now he just wanted to curl up on the couch with Peter and Pepper and watch a Disney movie and just forget for one night. When he got to Queens to pick up his son, May gave him a sympathetic look and told him that Peter had been in bed with a terrible migraine ever since he’d left.

Tony wandered into Peter’s room and found a pile of blankets on the bed in the near pitch black room, his son’s foot poking out from the end.  
“Pete?” Tony asked softly. He received a groan in return.  
“Dad?”  
“Hey kiddo. You’re not feeling too good, huh?”  
“Hmmm, loud. Bright.”  
“Okay, how about I take you back to the tower and we get you into one of Uncle Bruce’s sensory deprivation pods?” Peter poked his head out and nodded. 

They were probably both too old for Tony to be carrying Peter, but the boy was small for his age and Tony was felt sorry that he was feeling so unwell and didn’t want to make him walk. May gave them both a kiss on the cheek as they left, Ben gave them both a gentle pat on the back. Peter was sleeping fitfully within 5 minutes of being in the car. 

Peter spent 24 hours in sensory deprivation, Tony figured he was catching up on some much needed sleep. Peter wandered into Tony’s lab that evening, greeting his dad – who hadn’t noticed him approaching – with a hug.  
“How’re you feeling, Pete?”  
“Better. Everything’s still a little intense but it doesn’t hurt anymore.” Tony froze. Something was off but he couldn’t place it. Peter didn’t notice his dad’s hesitation and kept talking. “What’re you working on?” Tony looked up at his son in shock.  
“Say that again.” Peter looked confused.  
“What are you working on?” he asked again, slowly.  
“Pete, your voice. You- you’re not stuttering.” It was true, the boy’s voice hadn’t been this clear since he was 7.  
“I’m not?” he was very confused, he hadn’t noticed it.  
“Yeah. Let’s go down to the med bay, I wanna run a couple of tests.” 

Internally, Tony was panicking. He wished he knew where Banner was because he was completely out of his depth. He didn’t say anything to Peter, not wanting to freak him out further, but he’d noticed that Peter easily kept pace with him as they walked through the tower; no sign of a limp at all. Something was definitely up.

This couldn’t be right. Tony had performed a CT scan on Peter and was confused at what he was seeing. Or rather, what he wasn’t seeing. Tony was far more used to looking at his son’s brain than he would like to be. Ever since the Obie incident several years ago, Tony had seen many scans of Peter’s brain and knew exactly which parts of it were damaged. But now? He was looking at a perfectly healthy brain. This went way above his field of knowledge. Trying not to concern Peter, he told him that he wasn’t sure what was going on, but they’d have another look the next day. As soon as Peter went to bed, he called Helen Cho.

Helen was as baffled as he was, which scared Tony even more. As far as she could tell, there wasn’t even any evidence that the brain had once been damaged and then repaired itself, it was like it had never been damaged in the first place. It wasn’t until she compared a few different DNA samples with ones that Tony had on file that she noticed it.  
“Tony, can you come look at this?” She said nothing while he looked at the two different sets of DNA.  
“Alright boss, what am I supposed to be looking at? He asked.  
“I want you to tell me what you see?”  
“Okay, well. There’s two different sets of DNA, I assume one of these is Peter, whose is the other one?” She looked up at him with a serious face.  
“It’s Peter. Both of these are from Peter.” For just a moment, Tony forgot how to breathe.  
“How- How is that possible?” She looked at him with pity in her eyes.  
“If you weren’t so stunned, I think you would’ve figured it out already. There’s only one thing I know of that could alter a person’s DNA like this. I think he’s been injected with a super soldier serum.”

Tony called May and Ben first.  
“May? I hope I haven’t disturbed you.”  
“Not at all Tony, what’s going on?”  
“Something’s uh – something’s up with Peter. Nothing bad, I think. I just – has he had any shots lately that I don’t know about? Immunisations?”  
“Wh- no? Why?” Tony ignored her.  
“Any bug bites or anything?”  
“No, I- wait. He did say something about a spider bite the other day, but Tony you have to tell me what’s going on.”  
“I uh, I took a couple of brain scans for Peter yesterday.”  
“Oh my god, is everything okay?”  
“Yeah, they were clear.”  
“Oh, well that’s good, isn’t it?”  
“No, it was completely clear. I’m looking at scans of a perfectly healthy brain.” She didn’t say anything. “I called in someone who’s worked with us in the past and she found something in Peter’s DNA. It was completely different.”  
“What? How is that possible?”  
“We think he was injected with some sort of super soldier serum. Possibly through that spider bite.” She took a deep breath.  
“So what does all of this mean?”  
“I don’t know. I’m gonna figure it out though and I promise I’ll keep you updated.”

He called Steve next. He still hadn’t told Peter what was going on, he was too scared. He hoped that Steve would be willing to help him out. He, of course, was. When Tony told Steve what was going on, Steve attempted to comfort him by telling him that maybe all Peter had was some kind of enhanced healing. Tony let himself believe it, the alternative scared him too much. 

Peter had only met the other Avengers a couple of times. Much to his father’s dismay, he was a big fan of Captain America – had been since before Cap had come out of the ice – and had almost fainted the first time they’d met. He liked the others too, but Cap was always his favourite; after Tony, of course. So perhaps Tony should’ve thought it through before springing Cap on him out of the blue later that day. 

Peter was sitting on the sofa, watching one of the Harry Potter movies, Tony didn’t know which. He and cap approached Peter from behind and Cap said hello. To say Peter was startled would be an understatement. Peter jumped about 10 feet high. Literally. He had somehow landed on the roof and was clinging onto dear life up there.  
“Daddy?!” He sounded terrified.  
“Pete! Hold on! We’ll- wait, how are you holding yourself up there?”  
“I- I don’t know? It’s like my fingers and toes are sticking on the ceiling.”  
“Do you think you can climb down the wall? We’ll be ready to catch you, just in case.” Steve interrupted. Tony looked at him in horror.  
“I’ll try.” Peter said before Tony could say anything.

Sure enough, Peter started clambering across the roof and then down the wall with relative ease. Once he reached the ground he all but collapsed into his father’s waiting arms, shaking with adrenaline. Tony and Cap led Peter back to the sofa, sat him down, and filled him in on everything. Then Cap took him in to one of the training levels Tony had in the tower so they could test Peter’s capabilities. Turns out Peter could do a lot more than stick to stuff. He was almost as strong as Cap for starters, which got a big laugh out of Tony when he almost won their arm wrestle. He was also extremely agile and had extremely quick reflexes. They were testing out his reflexes by pummelling basketballs at him to catch. By chance, they discovered that he also apparently has a kind of sixth sense for danger. Steve had thrown a ball at the same moment that Peter turned around to say something to his dad and the ball was going to hit him until he managed to dodge it at the last second without turning back around.

After that, things seemed to go back to a relative state of normal. For the first couple of weeks, Steve trained with Peter so he could learn to control his strength in normal situations, and the boy quickly adjusted to his new life. 

With everything that had happened in Lagos and the UN putting the pressure on the Avengers, Tony had been ignoring most of the alerts he’d gotten on his phone about a new vigilante running around Queens. The ones he did read said the guy mostly dealt with little stuff, so he left it alone. But one afternoon he finally decided to catch up on the news on this ‘Spider-Man’. A startling realisation came over him the more he read about this guy. 

That night, Tony snuck into Peter’s bedroom at 11pm and sure enough the boy wasn’t there. So he hid in the corner of the room, sitting on the floor responding to emails. At around 2am, Tony heard the window opening from the outside and quickly switched off his phone. Sure enough, Spider-Man crawled through the window moments later. Tony waited until Peter had taken off the mask before switching on the light.  
“You are so busted.”

**Author's Note:**

> ***DISCLAIMER: This is in no way intended to be ableist, the idea popped into my head that if the spiderbite could repair Peter's crappy eyesight, then could it repair a traumatic brain injury as well? Then boom, this fic was born***
> 
> Comments/kudos are amazing!
> 
> Follow/send prompts to my instagram @everydaytomholland :)


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